Hi again,
   I’m looking for the right way to store some user credentials in the galaxy 
session so that tools can work on behalf of the user with our repository.

Currently users have an API key and they need to upload it as a data item to 
that is then passed to each tool that needs it as input.  This doesn’t seem 
like the right solution since the API key becomes part of the history and so 
would be shared if the history were shared.

What would be better would be a way of storing the API key in the user session 
and then being able to pass that into a tool.

I note that there are a few user session variables available in the tool xml 
file: __user__, __user_email__, __user_name__ and __user_id__.  There is also a 
user preferences page where they can fill out a few details.  However, I can’t 
see a mechanism to extend this in any way and have extra properties in the 
preferences pane that would then be available to tools via the template file.

I can see that the standard practice for the data sources on 
usegalaxy.org<http://usegalaxy.org> is to send the user off to a repository 
website to find data that is then posted back to the galaxy server.  This isn’t 
appropriate for us since the interaction with the repository is not just for 
downloading a single dataset - tools will query the repository, download 
various kinds of data and possibly upload new data, so we need to store user 
credentials in some way.

Is there already a good way to achieve this or is this an enhancement to Galaxy?



Department of Computing, Macquarie University

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